Summary
Square Bin
Cell Bin
Image

Spatial Gene Expression Distribution

Spatial gene expression distribution plot shows MID count at each spot (bin200)

Tissue Plot with Spot (bin200) Colored by MID Count

2,001,798,337

Total Reads

30,791

Mean MID per Bin200

5,945

Mean Gene Type per Bin200

119,151,481

Unique Reads

Key Metrices

Total Reads

Total number of sequenced reads

Valid CID Reads

Number of reads with CIDs matching the mask file and with MIDs passing QC

Invalid CID Reads

Number of reads with CIDs that cannot be matched with the mask file

Discarded MID Reads

Number of reads with MID that have been discarded since MID sequence quality does not satisfy with further analysis

Clean Reads

Number of Valid CID Reads that have passed QC

Non-Relevant Short Reads

Number of non-relevant short reads

Uniquely Mapped Reads

Number of reads that mapped uniquely to the reference genome

Multi-Mapped Reads

Number of reads that mapped more than one time on the genome

Unmapped Reads

Number of reads that cannot be mapped to the reference genome

Transcriptome

Number of reads that are aligned to transcripts of at least one gene

Unannotated Reads

Number of reads that cannot be aligned to transcript of one gene (intergenic)

Unique Reads

Number of reads in Transcriptome that have been corrected by MAPQ and deduplicated

Sequencing Saturation

Number of reads in Transcriptome that have been corrected by MAPQ with duplicated MID

Total Reads

100%

2,001,798,337

Valid CID Reads

80.1%

1,603,286,594

Clean Reads

64.3%

1,031,377,942

Uniquely Mapped Reads

77.8%

801,923,926

Transcriptome

79.9%

640,655,921

Unique Reads

18.6%

119,151,481

Sequencing Saturation

81.4%

521,504,440

Unannotated Reads

20.1%

161,268,005

Multi-Mapped Reads

15.1%

155,639,584

Unmapped Reads

7.2%

73,814,432

Non-Relevant Short Reads

35.7%

571,908,652

Invalid CID Reads

17.3%

346,042,187

Discarded MID Reads

2.6%

52,469,556

Information

Species

mouse

Tissue

brain

Reference

mouse

FASTQ

E200006028_L01_90_1 E200006028_L01_95_1
E200006028_L01_92_1 E200006028_L01_89_1
E200006028_L01_93_1 E200006028_L01_96_1
E200006028_L01_94_1 E200006028_L01_91_1

Sequencing

Total Reads

Total number of sequenced reads

Total Q30

Ratio of bases with quality value exceeded 30 in the sequenced reads

CID Q30

Ratio of CID (Coordinate ID) bases with quality value exceeded 30

MID Q30

Ratio of MID (Molecule ID) bases with quality value exceeded 30

Total Reads

2,001,798,337

Total Q30

95.66%

CID Q30

92.63%

MID Q30

90.19%

Annotation

Exonic

Number of reads that mapped uniquely to an exonic region and on the same strand of the genome

Intronic

Number of reads that mapped uniquely to an intronic region and on the same strand of the genome

Intergenic

Number of reads that mapped uniquely to an intergenic region and on the same strand of the genome

Transcriptome

Number of reads that mapped to a unique gene in the transcriptome. These reads are considered for MID counting. (Transcriptome = Exonic + Intronic)

Antisense

Number of reads mapped to the transcriptome but on the opposite strand of their annotated gene

Exonic

593,398,213

Intronic

47,257,708

Intergenic

161,268,005

Transcriptome

640,655,921

Antisense

165,645,501

RNA Mapping

Clean Reads

Number of Valid CID Reads that have passed QC

Uniquely Mapped Reads

Number of reads that mapped uniquely to the reference genome

Multi-Mapped Reads

Number of reads that mapped more than one time on the genome

Unmapped Reads

Number of reads that cannot be mapped to the reference genome

Clean Reads

1,031,377,942

Uniquely Mapped Reads

801,923,926

Multi-Mapped Reads

155,639,584

Unmapped Reads

73,814,432

Tissue Segmentation

Tissue

DNB Under Tissue

Number of DNBs under tissue coverage region

mRNA-Captured DNBs Under Tissue

Number of DNBs under tissue that have captured mRNA

Genes Under Tissue

Number of detected gene under tissue coverage

Number of MID Under Tissue Coverage

Number of MID under tissue coverage

Fraction MID in Spots Under Tissue

Fraction of MID under tissue over total unique reads (MID Under Tissue / Unique Reads)

Reads Under Tissue

Number of reads with position prior to filtration under tissue coverage

Fraction Reads in Spots Under Tissue

Fraction of mapped reads under tissue over total mapped reads (Mapped Reads in Spots Under Tissue / (Valid CID Reads + Discarded MID Reads))

DNB Under Tissue

97,619,419

mRNA-Captured DNBs Under Tissue

36,416,923

Genes Under Tissue

34,610

Number of MID Under Tissue Coverage

79,472,853

Fraction MID in Spots Under Tissue

66.70%

Reads Under Tissue

845,349,512

Fraction Reads in Spots Under Tissue

51.06%

Sequencing Saturation

(left) Plot of the sequencing saturation as a function of sequencing depth(bin200)

(middle) Plot of the median number of genes detected per bin as a function of sequencing depth(bin200)

(right) Plot of the unique reads detected per bin as a function of sequencing depth(bin200)

Tissue Square Bin Statistics

Bin Size

The size of Bin which is the unit of aggregated DNBs in a squared region (i.e. Bin 50 = 50 * 50 DNBs)

Mean Reads (per bin)

Mean number of sequenced reads divided by the number of bins under tissue coverage

Median Reads (per bin)

Median number of sequenced reads divided by the number of bins under tissue coverage (pick the middle value after sorting)

Mean Gene Type (per bin)

Mean number of unique gene types divided by the number of bins under tissue coverage

Median Gene Type (per bin)

Median number of unique gene types divided by the number of bins under tissue coverage

Mean MID (per bin)

Mean number of MIDs divided by the number of bins under tissue coverage

Median MID (per bin)

Median number of MIDs divided by the number of bins under tissue coverage

Bin Size

Mean Reads
(per bin)

Median Reads
(per bin)

Mean Gene Type
(per bin)

Median Gene Type
(per bin)

Mean MID
(per bin)

Median MID
(per bin)

14.26

1.57

2.18

3,443

3,327

199

197

323

315

21,331

21,014

973

985

2,005

1,987

100

84,114

83,926

2,687

2,761

7,907

7,916

150

186,570

188,536

4,410

4,573

17,543

17,730

200

327,527

331,773

5,945

6,202

30,791

31,230

Bin 20

(left) Scatter plot of MID count and gene types in each bin

(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin

(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis

Bin 50

(left) Scatter plot of MID count and gene types in each bin

(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin

(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis

Bin 100

(left) Scatter plot of MID count and gene types in each bin

(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin

(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis

Bin 150

(left) Scatter plot of MID count and gene types in each bin

(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin

(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis

Bin 200

(left) Scatter plot of MID count and gene types in each bin

(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin

(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis

Clustering

(left) Clustering spots (bin200) under tissue covered with the Leiden algorithm

(right) UMAP projections of spots (bin200) colored by automated clustering. Same color is assigned to spots that are within shorter distance and with similar gene expression profile

Tissue Plot with Spots (bin200)

UMAP Projection of Spots (bin200)

Cell Bin Statistics

Cell Count

Number of cells

Mean/Median Cell Area

Mean/Median cell area (pixel)

Mean/Median DNB Count

Mean/Median number of DNBs that have captured-mRNAs per cell

Mean/Median Gene Type

Mean/Median gene types per cell

Mean/Median MID

Mean/Median MID count per cell

Cell Count

53,702

Mean Cell Area

921

Median Cell Area

893

Mean DNB Count

365

Median DNB Count

344

Mean Gene Type

454

Median Gene Type

426

Mean MID

828

Median MID

749

Cell Bin

(left) Scatter plot of MID count and gene types in each bin

(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin

(bottom) Univariate distribution of MID count, gene types, DNB numbers, and cell area (pixel) with rug along the x axis

Clustering

(left) Clustering spots (cell bin) under tissue covered region with the Leiden algorithm

(right) UMAP projections of spots (cell bin) colored by automated clustering. Spots in the short distance are assigned with the same color have similar gene expression profile.

Tissue Plot with Spots (cell bin)

UMAP Projection of Spots (cellbin)

Image Information

Manufacture

Zeiss

Model

Scan Time

Overlap

0.1

Exposure Time (ms)

-999.999

Scan Rows

Scan Columns

FOV Height

2,000

FOV Width

2,000

Stain Type

ssDNA

Stitched Image

Yes

Image Name

D02674A3_SC_20231109_092548_3.0.0

Stitching

Template Source Row No.

The row number of the template FOV used for predicting the entire template

Template Source Column No.

The column number of the template FOV used for predicting the entire template

Global Height

Height of the stitched image

Global Width

Width of the stitched image

Template Source Row No.

Template Source Column No.

Global Height

17,216

Global Width

17,541

ImageQC version

QC Pass

Whether the image(s) passed imageQC quality check

Track Line Score

Reference score for track line detection

Clarity Score

Reference score for image clarity

Good FOV Count

Number of FOVs that have at least one track dot detected

Total FOV Count

Total number of FOVs

Stitching Score

Reference score for stitching

Tissue Segmentation Score

Reference score for tissue segmentation

Registration Score

Reference score for auto-aligning image with gene expression matrix

ImageQC Version

3.0.0

QC Pass

Pass

Track Line Score

Clarity Score

Good FOV Count

Total FOV Count

Stitching Score

Tissue Segmentation Score

Registration Score

Registration

ScaleX

The lateral scaling between image and template

ScaleY

The longitudinal scaling between image and template

Rotation

The rotation angle of the image relative to the template

Flip

Whether the image is flipped horizontally

Image X Offset

Offset between image and matrix in x direction

Image Y Offset

Offset between image and matrix in y direction

Counter Clockwise Rotation

Counter clockwise rotation angle

Manual ScaleX

The lateral scaling based on image center (manual-registration)

Manual ScaleY

The longitudinal scaling based on image center (manual-registration)

Manual Rotation

The rotation angle based on image center (manual-registration)

Matrix X Start

Gene expression matrix offset in x direction by DNB numbers

Matrix Y Start

Gene expression matrix offset in y direction by DNB numbers

Matrix Height

Gene expression matrix height

Matrix Width

Gene expression matrix width

ScaleX

0.806

ScaleY

0.806

Rotation

0.777

Flip

True

Image X Offset

1,904

Image Y Offset

5,210

Manual ScaleX

Manual ScaleY

Manual Rotation

Counter Clockwise Rotation

180

Matrix X Offset

0.00

Matrix Y Offset

0.00

Matrix Height

26,460

Matrix Width

26,460

Global Image Stitching Deviation Heatmap

Image stitching deviation, a lighter color indicates better stitching(the heatmap and frame of axes have been adjusted with the registration parameters)